Variant report

Variant	rs829811
Chromosome Location	chr6:110014882-110014883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10872036	0.83[ASN][1000 genomes]
rs10872037	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10872038	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1096137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1096141	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1103996	0.91[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11153186	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11153196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1115978	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12175588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12191099	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12194431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12209401	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12216333	0.88[ASN][1000 genomes]
rs1321206	0.83[ASN][1000 genomes]
rs1321208	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1406955	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17070673	0.83[ASN][1000 genomes]
rs1923057	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2025149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2884130	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799852	0.90[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3823234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4945834	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4945838	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946985	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946990	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4947005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4947007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4947013	0.95[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4947014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947020	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62435962	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6899688	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6899915	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6906729	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6912209	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6921615	0.90[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6933962	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6936853	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6941211	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7757153	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7757895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7759120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7763229	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7764711	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7770807	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7771150	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7772817	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7775414	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829810	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829812	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs865503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs866685	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9285400	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9320293	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9320301	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9372223	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9374104	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9374105	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9374111	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9374112	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9374120	0.80[ASN][1000 genomes]
rs9384712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9384719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9386811	0.83[ASN][1000 genomes]
rs9386815	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9386819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9386822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9386828	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9386829	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398210	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9398212	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9400292	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9400298	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9400302	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9480972	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9480980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487132	0.95[CEU][hapmap]
rs9487161	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487181	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487182	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9487211	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9766863	0.95[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829811	AKD1	cis	cerebellum	SCAN
rs829811	RFPL4B	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110011200-110015000	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr6:110012800-110015000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr6:110013000-110015000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:110013000-110022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:110013000-110022400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:110013000-110023600	Weak transcription	Gastric	stomach
7	chr6:110013000-110024800	Weak transcription	Lung	lung
8	chr6:110013000-110025200	Weak transcription	Small Intestine	intestine
9	chr6:110013000-110027400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:110013000-110027400	Weak transcription	Spleen	Spleen
11	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
12	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
13	chr6:110013200-110015000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr6:110013200-110015000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:110013200-110015000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:110013200-110020200	Weak transcription	Colonic Mucosa	Colon
17	chr6:110013200-110022200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:110013200-110022400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:110013200-110024200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:110013200-110026400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:110013200-110026600	Weak transcription	Ovary	ovary
22	chr6:110013200-110034000	Weak transcription	Fetal Stomach	stomach
23	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
25	chr6:110013400-110015000	Enhancers	Primary hematopoietic stem cells	blood
26	chr6:110013400-110015000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:110013400-110015000	Enhancers	Fetal Brain Female	brain
28	chr6:110013400-110022200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:110013400-110023200	Weak transcription	Fetal Intestine Large	intestine
30	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:110013600-110015000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:110013600-110015000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:110013600-110015000	Enhancers	Brain Hippocampus Middle	brain
34	chr6:110013600-110015000	Flanking Active TSS	GM12878-XiMat	blood
35	chr6:110013600-110016600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:110013600-110017200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:110013600-110017200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:110013600-110018600	Weak transcription	Osteobl	bone
39	chr6:110013600-110022200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:110013600-110022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:110013600-110022600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:110013800-110016600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:110013800-110018000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:110013800-110018600	Weak transcription	NHDF-Ad	bronchial
47	chr6:110013800-110026400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:110013800-110026600	Weak transcription	Brain Substantia Nigra	brain
49	chr6:110013800-110029600	Weak transcription	Fetal Lung	lung
50	chr6:110014000-110017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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